5-151674576-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003118.4(SPARC):c.120+36T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,604,502 control chromosomes in the GnomAD database, including 25,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2677 hom., cov: 32)
Exomes 𝑓: 0.16 ( 22989 hom. )
Consequence
SPARC
NM_003118.4 intron
NM_003118.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.716
Genes affected
SPARC (HGNC:11219): (secreted protein acidic and cysteine rich) This gene encodes a cysteine-rich acidic matrix-associated protein. The encoded protein is required for the collagen in bone to become calcified but is also involved in extracellular matrix synthesis and promotion of changes to cell shape. The gene product has been associated with tumor suppression but has also been correlated with metastasis based on changes to cell shape which can promote tumor cell invasion. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 5-151674576-A-C is Benign according to our data. Variant chr5-151674576-A-C is described in ClinVar as [Benign]. Clinvar id is 1242259.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPARC | NM_003118.4 | c.120+36T>G | intron_variant | ENST00000231061.9 | |||
SPARC | NM_001309443.2 | c.117+36T>G | intron_variant | ||||
SPARC | NM_001309444.2 | c.120+36T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARC | ENST00000231061.9 | c.120+36T>G | intron_variant | 1 | NM_003118.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26468AN: 151990Hom.: 2674 Cov.: 32
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GnomAD3 exomes AF: 0.211 AC: 52771AN: 250540Hom.: 7303 AF XY: 0.202 AC XY: 27372AN XY: 135426
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GnomAD4 exome AF: 0.162 AC: 236000AN: 1452394Hom.: 22989 Cov.: 29 AF XY: 0.163 AC XY: 118008AN XY: 723268
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GnomAD4 genome AF: 0.174 AC: 26489AN: 152108Hom.: 2677 Cov.: 32 AF XY: 0.179 AC XY: 13310AN XY: 74346
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 25, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at